Symptoms
Order is stuck in Waiting for Payment status. On Documents tab of the order you see the invoice applied to the order, but Applied Amount is different for 0.01 from Total Amount of the order.
Cause
The issue when Tax applied to the Order has parameter Calculation Type(Home>Configuration Director>Sales & Financial Settings>Taxes>[tax]) set to Document. In this case tax for order is calculated in following way:
OrderTax = rounding(([sum of extended value of all order lines])*tax)
But when consolidated invoice is generated tax is calculated in following way:
InvoiceTax = sum(rounding([extended value of each order line]*tax))
Thus in some case it may happen that OrderTax is not equal to InvoiceTax.
Resolution
The issue was reported to developers in internal request #PBA-37459. The issue was fixed in PBA-E 5.5, please upgrade to the latest version of PBA-E.
If upgrade is not possible at the moment you can change Calculation Type to Item. In this case calculation algorithm for Order and Invoice taxes will be the same.